Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties

Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.

Effects of Micro-Topography and Vegetation on Soil Moisture on Fixed Sand Dunes in Tengger Desert, China

Soil moisture is a key factor in arid ecosystems, with local variations influenced by topography and vegetation. Understanding this relationship is crucial for combating desertification. Employing ANOVA, Mean Decrease Accuracy (MDA) analysis from random forest modeling and Structural Equation Modeling (SEM), this study investigates the distribution of soil moisture and its associations with topographic and vegetative factors across four micro-geomorphic units in the Tengger Desert, China. Significant heterogeneity in soil moisture across various layers and locations, including windward and leeward slopes and the tops and bottoms of dunes, was observed. Soil moisture generally increases from the surface down to 300 cm, with diminishing fluctuations at greater depths. Soil moisture peaks in the surface and middle layers on windward slopes and in deep layers at the bottom of dunes, exhibiting an initial rise and then a decline on windward slopes. Topographic (including slope direction and elevation difference) and vegetation (including shrub and herb coverage) factors significantly influence soil moisture across three depth layers. Topographic factors negatively affect soil moisture directly, whereas vegetation positively influences it indirectly, with shrub and herb abundance enhancing moisture levels. These insights inform ecological management and the formulation of soil moisture-conservation strategies in arid deserts. The study underscores customizing sand-binding vegetation to various micro-geomorphic dune units.

Mycorrhizal fungi modify decomposition: a meta-analysis

It has been proposed that ectomycorrhizal fungi can reduce decomposition while arbuscular mycorrhizal fungi may enhance it. These phenomena are known as the 'Gadgil effect' and 'priming effect', respectively. However, it is unclear which one predominates globally. We evaluated whether mycorrhizal fungi decrease or increase decomposition, and identified conditions that mediate this effect. We obtained decomposition data from 43 studies (97 trials) conducted in field or laboratory settings that controlled the access of mycorrhizal fungi to substrates colonized by saprotrophs. Across studies, mycorrhizal fungi promoted decomposition of different substrates by 6.7% overall by favoring the priming effect over the Gadgil effect. However, we observed significant variation among studies. The substrate C : N ratio and absolute latitude influenced the effect of mycorrhizal fungi on decomposition and contributed to the variation. Specifically, mycorrhizal fungi increased decomposition at low substrate C : N and absolute latitude, but there was no discernable effect at high values. Unexpectedly, the effect of mycorrhizal fungi was not influenced by the mycorrhizal type. Our findings challenge previous assumptions about the universality of the Gadgil effect but highlight the potential of mycorrhizal fungi to negatively influence soil carbon storage by promoting the priming effect.

Mycorrhizal associations relate to stable convergence in plant-microbial competition for nitrogen absorption under high nitrogen conditions

Nitrogen (N) immobilization (Nim, including microbial N assimilation) and plant N uptake (PNU) are the two most important pathways of N retention in soils. The ratio of Nim to PNU (hereafter Nim:PNU ratio) generally reflects the degree of N limitation for plant growth in terrestrial ecosystems. However, the key factors driving the pattern of Nim:PNU ratio across global ecosystems remain unclear. Here, using a global data set of 1018 observations from 184 studies, we examined the relative importance of mycorrhizal associations, climate, plant, and soil properties on the Nim:PNU ratio across terrestrial ecosystems. Our results show that mycorrhizal fungi type (arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) fungi) in combination with soil inorganic N mainly explain the global variation in the Nim:PNU ratio in terrestrial ecosystems. In AM fungi-associated ecosystems, the relationship between Nim and PNU displays a weaker negative correlation (r = -.06, p < .001), whereas there is a stronger positive correlation (r = .25, p < .001) in EM fungi-associated ecosystems. Our meta-analysis thus suggests that the AM-associated plants display a weak interaction with soil microorganisms for N absorption, while EM-associated plants cooperate with soil microorganisms. Furthermore, we find that the Nim:PNU ratio for both AM- and EM-associated ecosystems gradually converge around a stable value (13.8 ± 0.5 for AM- and 12.1 ± 1.2 for EM-associated ecosystems) under high soil inorganic N conditions. Our findings highlight the dependence of plant-microbial interaction for N absorption on both plant mycorrhizal association and soil inorganic N, with the stable convergence of the Nim:PNU ratio under high soil N conditions.

Simulated nitrogen load promoted mineralization of N2P1 compounds and accumulation of N4S2 compounds in soil dissolved organic matter in a typical subtropical estuarine marsh

Soil dissolved organic matter (DOM) is the most reactive pool in estuarine marshes, playing an important role in the biogeochemical processes of biogenetic elements. To investigate the impacts of enhanced nitrogen (N) load on DOM molecular composition and its interactions with microbes in typical Cyperus malaccensis mashes of the Min River estuary, a field N load experiment with four N levels (0, 37.50, 50 and 100 g exogenous N m-2 yr-1, respectively; applied monthly for a total of seven months) was performed. DOM molecular composition was characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), the microbial community compositions (MCC, including fungi and bacteria) were determined by high-throughput sequencing technique, and their relationships were presented by co-occurrence network analysis. The results indicated that enhanced N load had significant impacts on soil DOM molecular composition, with N/C and P/C of DOM decreasing but S/C increasing markedly. Meanwhile, enhanced N load decreased the percentages of N2P1 compounds (primarily lipids) but increased those of N4S2 compounds (mainly lignins and lipids). The relative abundances of lignins significantly increased with increasing N load levels, whereas the proportions of lipids decreased. The abundance of N2P1 and N4S2 compounds was primarily positively correlated with eutrophic and oligotrophic microorganisms, respectively. Therefore, mineralization of N2P1 compounds might act as a source to replenish inorganic P, while enrichment of N4S2 compounds may make great contribution to organic S accumulation. Overall, enhanced N load promoted P depletion and S enrichment via altering plant growth, litter decomposition and MCC.

Soil stoichiometric imbalances constrain microbial-driven C and N dynamics in grassland

Grassland restoration leads to excessive soils with carbon (C) and nitrogen (N) contents that are inadequate to fulfill the requirements of microorganisms. The differences in the stoichiometric ratios of these elements could limit the activity of microorganisms, which ultimately affects the microbial C, N use efficiencies (CUE, NUE) and the dynamics of soil C and N. The present study was aimed at quantifying the soil microbial nutrient limitation and exploring the mechanisms underlying microbial-induced C and N dynamics in chrono-sequence of restored grasslands. It was revealed that grassland restoration increased microbial C, N content, microbial C, N uptake, and microbial CUE and NUE, while the threshold elemental ratio (the C:N ratio) decreased, which is mainly due to the synergistic effect of the microbial biomass and enzymatic stoichiometry imbalance after grassland restoration. Finally, we present a framework for the nutrient limitation strategies that stoichiometric imbalances constrain microbial-driven C and N dynamics. These results are the direct evidence of causal relations between stoichiometric ratios, microbial responses, and soil C, N cycling.

Assessing ammonium pollution and mitigation measures through a modified watershed non-point source model

Watershed water quality modeling is a valuable tool for managing ammonium (NH4+) pollution. However, simulating NH4+ pollution presents unique challenges due to the inherent instability of NH4+ in natural environment. This study modified the widely-used Soil and Water Assessment Tool (SWAT) model to simulate non-point source (NPS) NH4+ processes, specifically incorporating the simulation of land-to-water NH4+ delivery. The Jiulong River Watershed (JRW) is the study area, a coastal watershed in Southeast China with substantial sewage discharge, livestock farming, and fertilizer application. The results demonstrate that the modified model can effectively simulate the NPS NH4+ processes. It is recommended to use multiple sets of observations to calibrate NH4+ simulation to enhance model reliability. Despite constituting a minor proportion (5.6 %), point source inputs significantly contribute to NH4+ load at watershed outlet (32.4∼51.9 %), while NPS inputs contribute 15.3∼17.3 % of NH4+ loads. NH4+ primarily enters water through surface runoff and lateral flow, with negligible leaching. Average NH4+ land-to-water delivery rate is about 2.35 to 2.90 kg N/ha/a. High delivery rates mainly occur at agricultural areas. Notably, proposed NH4+ mitigation measures, including urban sewage treatment enhancement, livestock manure management improvement, and fertilizer application reduction, demonstrate potential to collectively reduce the NH4+ load at watershed outlet by 1/4 to 1/3 and significantly enhance water quality standard compliance frequency. Insights gained from modeling experience in the JRW offer valuable implications for NH4+ modeling and management in regions with similar climates and significant anthropogenic nitrogen inputs.

Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation

Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.

Dynamics of nitrogen mineralization and fine root decomposition in sub-tropical Shorea robusta Gaertner f. forests of Central Himalaya, India

This study aimed to examine the effects of spatial and temporal variability in edaphic, and climatic attributeson soil net nitrogen mineralization rate, and to understand the pattern of fine root decomposition of dominant and co-dominant tree species, and its influence on the nutrient cycling in forest ecosystems. Study was carried out at four different sites in sub-tropical forest ecosystems of Shorea robusta, in foothills of Central Himalayan region, India. Co-dominant tree species at four sites were Mallotus philippensis (site A), Glochidion velutinum (site B), Holarrhena pubescens (site C), and Tectona grandis (site D). Buried bag technique was used for nitrogen mineralization, while fine root decomposition was determined using fine root mesh bags. Seasonal variation, soil depth, soil characteristics, and site variability, all significantly (p < 0.05) affected nitrogen mineralization rates. Fine root decomposition was significantly affected by nutrient concentration of fine roots. Total mineral nitrogen was maximum at site D (16.24 ± 0.96 μg g-1 soil), while minimum at site C (10.10 ± 0.84 μg g-1 soil). Maximum nitrogen mineralization (13.18 ± 0.18 μg g-1 month-1) was recorded during summer season at site D, while the minimum nitrogen mineralization (3.20 ± 0.46 μg g-1 month-1) was recorded during rainy season at site C. Inorganic-N and net nitrogen mineralization was relatively higher in 0-20 cm soil layer than 20-40 cm and 40-60 cm soil layer. The fine roots showed 70.61-74.82 % weight loss on completion of 365 days of decomposition process. Maximum fine root decomposition was observed in the G. velutinum, and minimum in T. grandis. A significant positive correlation (p < 0.05) was observed between root nitrogen and carbon content, and decomposition rates per month. This study concluded that the spatial and temporal variability in soil nitrogen mineralization rates and fine root decomposition optimises nutrient cycling in forest ecosystems, which can contribute to the development of sustainable forest management practices.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis

Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.

Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition

Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha-1 yr-1) and high (50 kg N ha-1 yr-1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.

Changes in soil oxidase activity induced by microbial life history strategies mediate the soil heterotrophic respiration response to drought and nitrogen enrichment

Drought and nitrogen deposition are two major climate challenges, which can change the soil microbial community composition and ecological strategy and affect soil heterotrophic respiration (Rh). However, the combined effects of microbial community composition, microbial life strategies, and extracellular enzymes on the dynamics of Rh under drought and nitrogen deposition conditions remain unclear. Here, we experimented with an alpine swamp meadow to simulate drought (50% reduction in precipitation) and multilevel addition of nitrogen to determine the interactive effects of microbial community composition, microbial life strategy, and extracellular enzymes on Rh. The results showed that drought significantly reduced the seasonal mean Rh by 40.07%, and increased the Rh to soil respiration ratio by 22.04%. Drought significantly altered microbial community composition. The ratio of K- to r-selected bacteria (BK:r) and fungi (FK:r) increased by 20 and 91.43%, respectively. Drought increased hydrolase activities but decreased oxidase activities. However, adding N had no significant effect on microbial community composition, BK:r, FK:r, extracellular enzymes, or Rh. A structural equation model showed that the effects of drought and adding nitrogen via microbial community composition, microbial life strategy, and extracellular enzymes explained 84% of the variation in Rh. Oxidase activities decreased with BK:r, but increased with FK:r. Our findings show that drought decreased Rh primarily by inhibiting oxidase activities, which is induced by bacterial shifts from the r-strategy to the K-strategy. Our results highlight that the indirect regulation of drought on the carbon cycle through the dynamic of bacterial and fungal life history strategy should be considered for a better understanding of how terrestrial ecosystems respond to future climate change.

Bacterial and fungal communities in sub-Arctic tundra heaths are shaped by contrasting snow accumulation and nutrient availability

Climate change is affecting winter snow conditions significantly in northern ecosystems but the effects of the changing conditions for soil microbial communities are not well-understood. We utilized naturally occurring differences in snow accumulation to understand how the wintertime subnivean conditions shape bacterial and fungal communities in dwarf shrub-dominated sub-Arctic Fennoscandian tundra sampled in mid-winter, early, and late growing season. Phospholipid fatty acid (PLFA) and quantitative PCR analyses indicated that fungal abundance was higher in windswept tundra heaths with low snow accumulation and lower nutrient availability. This was associated with clear differences in the microbial community structure throughout the season. Members of Clavaria spp. and Sebacinales were especially dominant in the windswept heaths. Bacterial biomass proxies were higher in the snow-accumulating tundra heaths in the late growing season but there were only minor differences in the biomass or community structure in winter. Bacterial communities were dominated by members of Alphaproteobacteria, Actinomycetota, and Acidobacteriota and were less affected by the snow conditions than the fungal communities. The results suggest that small-scale spatial patterns in snow accumulation leading to a mosaic of differing tundra heath vegetation shapes bacterial and fungal communities as well as soil carbon and nutrient availability.

Warming drives feedback between plant phenotypes and ecosystem functioning in sub-Antarctic ponds

Ample evidence indicates that warming affects individuals in plant communities, ultimately threatening biodiversity. Individual plants in communities are also exposed to plant-plant interaction that may affect their performance. However, trait responses to these two constraints have usually been studied separately, while they may influence processes at the ecosystem level. In turn, these ecological modifications may impact the phenotypes of plants through nutrient availability and uptake. We developed an experimental approach based on the macrophyte communities in the ponds of the sub-Antarctic Iles Kerguelen. Individuals of the species Limosella australis were grown under different temperature × plant-plant interaction treatments to assess their trait responses and create litters with different characteristics. The litters were then decomposed in the presence of individual plants at different temperatures to examine effects on ecosystem functioning and potential feedback affecting plant trait values. Leaf resource-acquisition- and -conservation-related traits were altered in the context of temperature × plant-plant interaction. At 13 °C, SLA and leaf C:N were higher under interspecific and intraspecific interactions than without interaction, whereas at 23 °C, these traits increased under intraspecific interaction only. These effects only slightly improved the individual performance, suggesting that plant-plant interaction is an additional selective pressure on individuals in the context of climate warming. The decay rate of litter increased with the Leaf Carbon Content at 13 °C and 18 °C, but decreased at 23 °C. The highest decay rate was recorded at 18 °C. Besides, we observed evidence of positive feedback of the decay rate alone, and in interaction with the temperature, respectively on the leaf C:N and Leaf Dry Matter Content, suggesting that variations in ecological processes affect plant phenotypes. Our findings demonstrate that warming can directly and indirectly affect the evolutionary and ecological processes occurring in aquatic ecosystems through plants.

N-fertilization and disturbance exert long-lasting complex legacies on subarctic ecosystems

Subarctic ecosystems are subjected to increasing nitrogen (N) enrichment and disturbances that induce particularly strong effects on plant communities when occurring in combination. There is little experimental evidence on the longevity of these effects. We applied N-fertilization (40 kg urea-N ha-1 year-1 for 4 years) and disturbance (removal of vegetation and organic soil layer on one occasion) in two plant communities in a subarctic forest-tundra ecotone in northern Finland. Within the first four years, N-fertilization and disturbance increased the share of deciduous dwarf shrubs and graminoids at the expense of evergreen dwarf shrubs. Individual treatments intensified the other's effect resulting in the strongest increase in graminoids under combined N-fertilization and disturbance. The re-analysis of the plant communities 15 years after cessation of N-fertilization showed an even higher share of graminoids. 18 years after disturbance, the total vascular plant abundance was still substantially lower and the share of graminoids higher. At the same point, the plant community composition was the same under disturbance as under combined N-fertilization and disturbance, indicating that multiple perturbations no longer reinforced the other's effect. Yet, complex interactions between N-fertilization and disturbance were still detected in the soil. We found higher organic N under disturbance and lower microbial N under combined N-fertilization and disturbance, which suggests a lower bioavailability of N sources for soil microorganisms. Our findings support that the effects of enhanced nutrients and disturbance on subarctic vegetation persist over decadal timescales. However, they also highlight the complexity of plant-soil interactions that drive subarctic ecosystem responses to multiple perturbations across varying timescales.

Potential future changes in soil carbon dynamics in the Ziwuling Forest, China under different climate change scenarios

Soil carbon (C) cycling processes in terrestrial ecosystems are significantly influenced by global changes, and soil microorganisms play a crucial role in soil organic carbon (SOC) and its feedbacks to climate change. To investigate the potential future changes in soil C dynamics under different scenarios in the Ziwuling Forest region, China, we conducted a soil observation and sampling experiment from April 2021 to July 2022. By utilizing a microbial ecological model (MEND), we aimed to predict the future dynamics of soil C under different scenarios in the area. Our results demonstrate that under the RCP2.6 (Representative Concentration Pathway) scenario, SOC showed a rapid increase, SOC under the RCP2.6 scenario will be significantly higher than those under the RCP4.5 scenario and RCP8.5 scenario in the topsoil and whole soil. Furthermore, the positive correlation between total litter carbon (LC) and SOC under the RCP2.6 scenario highlights the potential role of total litter carbon in driving SOC dynamics. Our study also revealed that the low greenhouse gas (GHG) emission scenario favors the accumulation of SOC in the study area, while the high GHG emission scenario leads to greater soil carbon loss. Overall, these results underscore the importance of considering the impact of climate change, especially global warming, on soil ecosystems in the future. Protecting the soil ecosystem of the Loess Plateau is critical for maintaining soil carbon sinks, preventing soil erosion, and improving and regulating the surrounding environmental climate.

Land Use Change from Natural Tropical Forests to Managed Ecosystems Reduces Gross Nitrogen Production Rates and Increases the Soil Microbial Nitrogen Limitation

Understanding the underlying mechanisms of soil microbial nitrogen (N) utilization under land use change is critical to evaluating soil N availability or limitation and its environmental consequences. A combination of soil gross N production and ecoenzymatic stoichiometry provides a promising avenue for nutrient limitation assessment in soil microbial metabolism. Gross N production via 15N tracing and ecoenzymatic stoichiometry through the vector and threshold element ratio (Vector-TER) model were quantified to evaluate the soil microbial N limitation in response to land use changes. We used tropical soil samples from a natural forest ecosystem and three managed ecosystems (paddy, rubber, and eucalyptus sites). Soil extracellular enzyme activities were significantly lower in managed ecosystems than in a natural forest. The Vector-TER model results indicated microbial carbon (C) and N limitations in the natural forest soil, and land use change from the natural forest to managed ecosystems increased the soil microbial N limitation. The soil microbial N limitation was positively related to gross N mineralization (GNM) and nitrification (GN) rates. The decrease in microbial biomass C and N as well as hydrolyzable ammonium N in managed ecosystems led to the decrease in N-acquiring enzymes, inhibiting GNM and GN rates and ultimately increasing the microbial N limitation. Soil GNM was also positively correlated with leucine aminopeptidase and β-N-acetylglucosaminidase. The results highlight that converting tropical natural forests to managed ecosystems can increase the soil microbial N limitation through reducing the soil microbial biomass and gross N production.

©Relationship between endophytic fungal diversity and colonization and soil factors of cultured blueberry roots in Guizhou Province, Southwest China

Dark septate endophytes (DSEs) inhabit plant roots and soil in ecosystems and host plants worldwide. DSE colonization is influenced by cultivars, soil factors, and specific habitat conditions. The regular diversity of DSEs in blueberries in Guizhou, China, is still unclear. In this study, four cultivars (Gardenblue, Powderblue, O'Neal, and Legacy) in three areas (Gaopo, Majiang, and Fenggang) in Guizhou were used to identify DSEs by morphological and molecular biological methods and to clarify the relationship between DSE diversity and DSE colonization and soil factors of cultivated blueberries in Guizhou. The DSEs isolated from cultivated blueberry roots in 3 areas in Guizhou Province were different, belonging to 17 genera, and the dominant genera were Penicillium, Phialocephala, and Thozetella. DSEs isolated from Majiang belonged to 12 genera and 16 species, those from Gaopo belonged to 7 genera and 15 species, and those from Fenggang belonged to 5 genera and 7 species. Among the different blueberry varieties, 11 genera were isolated from O'Neal, 12 genera were isolated from Powderblue, 11 genera were isolated from Legacy and 13 genera were isolated from Gardenblue. Coniochaeta is endemic to O'Neal, Chaetomium and Curvularia are endemic to Powderblue, and Thielavia is endemic to Legacy. Correlation analysis showed that DSE diversity was significantly correlated with DSE colonization and soil factors.

Initial evidence on the effect of copper on global cropland nitrogen cycling: A meta-analysis

Copper (Cu) is a key cofactor in ammonia monooxygenase functioning responsible for the first step of nitrification, but its excess availability impairs soil microbial functions and plant growth. Yet, the impact of Cu on nitrogen (N) cycling and process-related variables in cropland soils remains unexplored globally. Through a meta-analysis of 1209-paired and 319-single observations from 94 publications, we found that Cu (Cu addition or Cu-polluted soil) reduced soil potential nitrification by 33.8% and nitrite content by 73.5% due to reduced soil enzyme activities of nitrification and urease, microbial biomass content, and ammonia oxidizing archaea abundance. The response ratio of potential nitrification decreased with increasing Cu concentration, soil total N, and clay content. We further noted that soil potential nitrification inhibited by 46.5% only when Cu concentration was higher than 150 mg kg-1, while low Cu concentration (less than 150 mg kg-1) stimulated soil nitrate by 99.0%. Increasing initial soil Cu content stimulated gross N mineralization rate due to increased soil organic carbon and total N, but inhibited gross nitrification rate, which ultimately stimulated gross N immobilization rate as a result of increased the residence time of ammonium. This resulted in a lower ratio of gross nitrification rate to gross N immobilization rate, implying a lower potential risk of N loss as evidenced by decreased nitrous oxide emissions with increasing initial soil Cu content. Our analysis offers initial global evidence that Cu has an important role in controlling soil N availability and loss through its effect on N production and consumption.

Reevaluation and novel insights into amino sugar and neutral sugar necromass biomarkers in archaea, bacteria, fungi, and plants

Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively.

Effect of a Fortified Biostimulant Extract on Tomato Plant Productivity, Physiology, and Growing Media Properties

The pursuit of sustainable and productive agriculture demands the exploration of innovative approaches to improve plant productivity and soil health. The utilization of natural agricultural biostimulants, such as extracts from seaweed, fish, and humus, has gained prominence as an ecological strategy to achieve this goal. In this study we investigated the effectiveness of a fortified biostimulant extract (FBE), composed of extracts from seaweed, fish, and humus, on tomato plant physiology, productivity, and growing media properties, and estimated carbon emissions associated with tomato production. The FBE was applied to the growing media of tomato plants produced in a greenhouse, in experiments over two growing seasons. The productivity assessments demonstrated that the application of FBE significantly increased tomato fruit yield by 20% and relative marketable fruit yield by 27%, and reduced estimated greenhouse gas (GHG) emissions associated with production by 29%. FBE treatment improved plant shoot and root biomass, accelerated flower and fruit set initiation, and increased chlorophyll content in leaves, resulting in enhanced plant physiology and advanced development. FBE treatment positively influenced the availability of crucial nutrients such as nitrogen, phosphorus, and iron in the growing media. FBE promoted the growth of total active microbes in the growing media, particularly the fungal population, which plays an important role in nutrient cycling and health. These findings highlight the beneficial effects of the FBE due to enhanced plant productivity and growth, improved fertility, the promotion of beneficial plant and growing media interactions, and the reduction in estimated GHG emissions.

N2O and CH4 fluxes from intensively managed grassland: The importance of biological and environmental drivers vs. management

Agriculture is the main contributor to anthropogenic nitrous oxide (N2O) and methane (CH4) emissions. Therefore, mitigation options are urgently needed. In contrast to carbon dioxide, eddy covariance measurements of N2O and CH4 fluxes are still scarce, and thus little is known how environmental and biotic drivers as well as management affect the net N2O and CH4 exchange in grasslands. Thus, we investigated the most important drivers of net ecosystem N2O and CH4 fluxes in a temperate grassland, and continued a N2O mitigation experiment (increased clover proportion vs. fertilization with slurry). Random forest gap-filling models were able to capture intermittent emission peaks, performing better for half-hourly N2O than for CH4 fluxes. The unfertilized clover parcel (parcel B) continued to show lower N2O emissions (4.4 and 2.7 kg N2O-N ha-1 yr-1) compared to the fertilized parcel (parcel A; 6.9 and 5.9 kg N2O-N ha-1 yr-1) for 2019 and 2020, respectively. Tier 1 nitrogen (N) emission factors of 2.6 % and 1.9 % were observed at the fertilized parcel during the study period. Lower soil N concentrations indicated a lower N leaching risk at the clover than at the fertilized parcel. Annual CH4 emissions (including periods with sheep grazing) were similar from both parcels, and ranged from 25 to 38.5 kg CH4-C ha-1. The most important drivers of both N2O and CH4 fluxes were lagged precipitation and water filled pore space, but also management (for N2O from parcel B; CH4 from parcel A). Biotic variables such as vegetation height and leaf area index were important predictors for the N2O exchange, while grazing temporarily increased CH4 emissions. Overall, reducing N fertilization and increasing the legume proportion were effective N2O reduction measures. In particular, adjusting N fertilization to plant N demands can help to avoid high N2O emissions from grasslands.

Dynamics of soil nitrogen availability following conversion of natural forests to various coffee cropping systems in northern Thailand

Land conversion critically affects soil physiochemical and biological properties, yet very little remains clear about the impact of forest conversion on the N pool and related microbial N transformations. Therefore, this study aimed to examine the dynamics of soil N availability following forest conversion into the different coffee cropping systems, and explore the mechanisms behind these dynamics from the microbial N transformation. Disturbed soil samples from two depths (0-20 and 20-40 cm) were collected from four land uses consisting of three different coffee cropping systems (coffee monocultures (C), coffee agroforestry (FC), coffee associated with persimmon (Diospyros kaki L.) (CH)) converted from natural forest and adjacent natural forest (F) in northern Thailand. The soil labile N pools (including ammonium (NH4+), nitrate (NO3-), inorganic N (IN), dissolved organic N (DON) contents and microbial biomass N (MBN)) were measured, as well as the soil total N (STN) content. Soil N transformation rates, including net N mineralization, nitrification, and immobilization, were determined using a laboratory incubation experiment. The results showed that the forest conversion to coffee agroforestry significantly increased soil N content by 39.83 % in topsoil, but no significant difference was observed in C and CH soils as compared to F soil (p ≤ 0.05). The three labile N forms (NH4+, NO3- and DON content) were significantly higher under the C, FC and CH soils in both depths, while the coffee monoculture decreased the MBN content. The increases in soil IN, IN/DON and NO3-/NH4+ ratios used as an N availability indicator were positively associated with an increase in the N mineralization and nitrification processes following the forest conversion. Interestingly, the N immobilization processes in the F and FC soils were significantly higher than those in the C and CH soils, which indirectly regulated a decreased nitrification rate in F and FC soils in our study. With the exception of the FC soil, the nitrification/N immobilization ratios in the C (4.95) and CH (4.08) soils were higher than those in the F (0.70) soil, indicating an increased N loss risk after forest conversion. Therefore, coffee agroforestry systems have the potential to be effective management strategies for improving soil nitrogen sequestration following forest conversion.

Epilithic biofilms provide large amounts of nitrogen to tropical mountain landscapes

We show that epilithic biofilms are a relevant nitrogen (N) source in a rocky mountain range in Brazil. During different seasons, we quantified nitrate, ammonium, dissolved organic N (DON) and total dissolved N (TDN) leached by a simulated short rain event. We quantified the epilithic autotrophic biomass by taxonomic groups and its correlation with leached N. We hypothesized that leached N would be correlated to heterocystous cyanobacteria biomass since they are more efficient N2 fixers. We estimated a landscape N supply of 8.5 kg.ha-1 .year-1 considering the mean precipitation in the region. TDN in leachate was mainly composed of DON (83.8% ± 22%), followed by nitrate (12.1% ± 3%) and ammonium (5% ± 5%). The autotrophic epilithic community was mainly composed of non-heterocystous (Gloeocapsopsis) and heterocystous cyanobacteria (Scytonema and Stigonema), except for a site more commonly affected by fire events that showed a dominance of Chlorophyta. Biogeochemical upscaling was facilitated by the fact that N leaching was not different among sites or related to autotrophic epilithic biomass or assemblage composition. In conclusion, the capacity of epilithic biofilms to provide N to surrounding systems is an ecosystem service that underscores the necessity to conserve them and their habitats.

Abundance and sources of organic nitrogen in fine (PM2.5) and coarse (PM2.5-10) particulate matter in urban Hong Kong

Organic nitrogen (ON) in atmospheric particles is much less monitored compared to inorganic nitrogen (IN), despite its significant contribution to atmospheric N deposition budget. In this study, we expanded a newly developed instrumental method for IN and ON in PM2.5 samples to PM10 samples. We determined the quantities of ON and IN for paired PM2.5 and PM10 samples collected at an urban coastal site in Hong Kong, southern China over a year. These measurements also allowed the determination of IN and ON abundance in the coarse PM (i.e., PM2.5-10) by taking the difference between PM10 and PM2.5. The measurement results show that ON accounted for 27.6 % and 21.1 % of total N in fine and coarse particles, respectively, and was mainly (87.7 %) distributed in the fine mode at the site. The seasonal variation of ON/total N was relatively small in PM2.5 (23.6-30.4 %) while considerably larger in coarse PM (4.3-42.1 %). Analysis aided by concurrently measured source indicators revealed that sea spray, biological particle emissions, and dust mixed with anthropogenic pollutants are potentially significant sources of ON in coarse particles. Positive matrix factorization (PMF) source apportionment further revealed that industrial emissions/coal combustion (43.6 %), soil dust emission (16.3 %), fresh sea salt emission (15.2 %), and aged sea salt (24.9 %) are major sources of PMcoarse-bound ON at the site. The contributions of industrial emissions/coal combustion and soil dust emission to ON were significantly higher in autumn and winter. Fresh sea salt emissions contributed greater proportions to ON in spring and summer, while ON associated with the aged sea salt source was higher in spring and autumn. These findings have advanced our quantitative understanding of the sources of PMcoarse-bound ON, which was scarcely determined in the past. Furthermore, the ON measurement data in fine and coarse particles helps estimate ON deposition, which has been previously under-evaluated.

The effect of afforestation type on soil nitrogen dynamics in the riparian zone of the upper Yangtze River of China

Afforestation is increasingly important in nutrient cycling in riparian ecotones given that ecosystems in riparian zones are susceptible to anthropogenic activities induced by land use change. However, how land use change (e.g., afforestation) with different planting types influences nitrogen (N) dynamics in riparian zones remains unclear. Here, we examined soil N dynamics following afforestation with three types of plantations of pure willow (Salix babylonica), pure mulberry (Morus alba), and the mixed two species paired with adjacent maize croplands in the upper Yangtze River of China. Our results showed afforestation with the two pure species significantly reduced soil total N (TN) concentration. Soil NO3--N concentration was significantly reduced by the willow and mixed-species afforestation, but soil NH4+-N concentration was significantly higher in the willow and mixed woodlands compared to the paired croplands. Soil N concentrations were tightly associated with the potential N transformation rates, which showed a roughly decreasing trend in N mineralization following afforestation. Soil properties, microbial biomass, and extracellular enzymes jointly explained a large proportion of the total variation in soil N concentrations, with soil enzymes largely contributing to N variation in the topsoil and soil properties primarily contributing to N variation in the subsoil. Overall, our results demonstrate that afforestation with different planting types had contrasting effects on soil N content in the riparian zone. These findings provide new insights into the management of afforestation types to retain soil N by mediating soil properties and microbial activities in the riparian zones under future land use change.

Mycorrhizal colonization had little effect on growth of Carex thunbergii but inhibited its nitrogen uptake under deficit water supply

BACKGROUND AND AIMS

Plant nitrogen (N) acquisition via arbuscular mycorrhizal fungi (AMF) serves as a dominant pathway in the N nutrition of many plants, but the functional impact of AMF in acquisition of N by wetland plants has not been well quantified. Subtropical lake-wetland ecosystems are characterized by seasonal changes in the water table and low N availability in soil. Yet, it is unclear whether and how AMF alters the N acquisition pattern of plants for various forms of N and how this process is influenced by soil water conditions.

METHODS

We performed a pot study with Carex thunbergii that were either colonized by AMF or not colonized and also subjected to different water conditions. We used 15N labelling to track plant N uptake.

KEY RESULTS

Colonization by AMF had little effect on the biomass components of C. thunbergii but did significantly affect the plant functional traits and N acquisition in ways that were dependent on the soil water conditions. The N uptake rate of AMF-colonized plants was significantly lower than that of the non-colonized plants in conditions of low soil water. A decreased NO3- uptake rate in AMF-colonized plants reduced the N:P ratio of the plants. Although C. thunbergii predominantly took up N in the form of NO3-, higher water availability increased the proportion of N taken up as NH4+, irrespective of the inoculation status.

CONCLUSIONS

These results emphasize the importance of AMF colonization in controlling the N uptake strategies of plants and can improve predictions of N budget under the changing water table conditions in this subtropical wetland ecosystem.

Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments

Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.

Exogenous Electroactive Microbes Regulate Soil Geochemical Properties and Microbial Communities by Enhancing the Reduction and Transformation of Fe(III) Minerals

Electroactive microbes can conduct extracellular electron transfer and have the potential to be applied as a bioresource to regulate soil geochemical properties and microbial communities. In this study, we incubated Fe-limited and Fe-enriched farmland soil together with electroactive microbes for 30 days; both soils were incubated with electroactive microbes and a common iron mineral, ferrihydrite. Our results indicated that the exogenous electroactive microbes decreased soil pH, total organic carbon (TOC), and total nitrogen (TN) but increased soil conductivity and promoted Fe(III) reduction. The addition of electroactive microbes also changed the soil microbial community from Firmicutes-dominated to Proteobacteria-dominated. Moreover, the total number of detected microbial species in the soil decreased from over 700 to less than 500. Importantly, the coexistence of N-transforming bacteria, Fe(III)-reducing bacteria and methanogens was also observed with the addition of electroactive microbes in Fe-rich soil, indicating the accelerated interspecies electron transfer of functional microflora.

Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass

Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological-spatial, temporal and phylogenetic-patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.

Higher N Addition and Mowing Interactively Improved Net Primary Productivity by Stimulating Gross Nitrification in a Temperate Steppe of Northern China

Anthropogenic disturbance, such as nitrogen (N) fertilization and mowing, is constantly changing the function and structure of grassland ecosystems during past years and will continue to affect the sustainability of arid and semiarid grassland in the future. However, how and whether the different N addition levels and the frequency of N addition, as well as the occurrence of mowing, affect the key processes of N cycling is still unclear. We designed a field experiment with five levels of N addition (0, 2, 10, 20, and 50 g N m^-2 yr^-1), two types of N addition frequencies (twice a year added in June/November and monthly addition), and mowing treatment in a typical grassland of northern China. The results showed that higher N addition and mowing interactively improved net primary productivity (NPP), including aboveground and belowground biomass, while different N addition frequency had no significant effects on NPP. Different N addition levels significantly improved gross ammonification (GA) and nitrification (GN) rates, which positively correlated to aboveground net primary productivity (ANPP). However, the effect of N addition frequency was differentiated with N addition levels, the highest N addition level (50 g N m^-2 yr^-1) with lower frequency (twice a year) significantly increased GA and GN rates. Mowing significantly increased the GA rate but decreased the GN rate both under the highest N addition level (50 g N m^-2 yr^-1) and lower N addition frequency (twice a year), which could improve N turnover by stimulating plant and microbial activity. However, a long-term study of the effects of N enrichment and mowing on N turnover will be needed for understanding the mechanisms by which nutrient cycling occurs in typical grassland ecosystems under global change scenarios.

Assessing the Effect of Slope Position on the Community Assemblage of Soil Diazotrophs and Root Arbuscular Mycorrhizal Fungi

Considering the crucial role of soil diazotrophs and root arbuscular mycorrhizal fungi (AMF) in soil nutrient cycling during ecosystem restoration, diazotroph and AMF communities may be determined by slope position. However, the effect of slope position on diazotroph and AMF abundance, diversity, and community composition of karst ecosystems remains unknown. In this study, soil diazotrophs and root AMF characteristics on varying slope positions were assessed in a karst shrub ecosystem. The results displayed that the abundance of soil diazotrophs and root AMF diversity were significantly affected by slope position. Diazotroph abundance accompanied by soil nutrient and plant richness was higher on the lower slopes than the upper slopes, whereas root AMF diversity displayed the opposite trend. The soil diazotroph and root AMF community composition differed among the upper, middle, and lower slopes. The dominant taxa of soil diazotrophs and root AMF at the order level were Rhizobiales and Glomerales, respectively. Moreover, the diazotroph order of Nostocales and the AMF order of Paraglomerales were richer on the upper slopes than on the lower slopes. The slope position directly affected the plant diversity and soil nutrient distribution, indirectly affecting the diazotroph and AMF communities. Increased available nitrogen on the lower slope caused great diazotroph abundance by stimulating plant growth with sufficient carbohydrates. However, low soil nutrients and plant diversity but high plant root biomass induced more root AMF diversity on the upper slope than on the lower slope. Therefore, this study expands the knowledge of soil diazotroph and root AMF ecological functions along different slope positions during vegetation recovery for the successive stages of grass and shrub in the karst region.

Soil texture is an easily overlooked factor affecting the temperature sensitivity of N2O emissions

As a potent greenhouse gas, soil nitrous oxide (N₂O) is strongly stimulated by rising temperature, triggering a positive feedback effect of global warming. However, its temperature sensitivity varies greatly among soils with different physical and chemical characteristics, while associated mechanisms remain unknown. Here we performed a meta-analysis of the effect of warming on N₂O emission and found distinctions in the response of N₂O to temperature increase in soils with different textures. Then, we conducted an incubation experiment on 11 arable soils with varying textures sampled across China. The results show that the temperature sensitivity of N₂O emissions was lower as soil texture became more clayey and was consistent with the outcome of meta-analysis. Further analysis was conducted by classifying the soils into clay and loam subgroups. As shown in the clay soil subgroup, N₂O emission was significantly correlated with both inorganic nitrogen contents and potential denitrification and nitrification activities. Correlation analysis and partial least square (PLS) path model revealed that temperature mediated N₂O emission by regulating nosZ gene abundance indirectly. In loam soils, however, the indirect effect of temperature on N₂O production was achieved mainly through nirS gene abundance. Additionally, soil DON content strongly correlated with N₂O emission in both subgroups and affected N₂O emissions by influencing the abundance of denitrifiers under warming conditions. Our findings suggest that (i) soil texture was an important factor affecting temperature sensitivity of N₂O emission and (ii) variable efficacy of warming in soil N₂O production might originate from the enriching DON and nitrate content and its different indirect effects on nirS- or nosZ-type denitrifiers.

Drought reduces invasive grass performance by disrupting plant-microbe interactions that enhance plant nitrogen supply

Non-native invasive plants can promote their dominance in novel ecosystems by accelerating soil nutrient cycling via interactions with decomposer microbes. Changes in abiotic conditions associated with frequent or prolonged drought may disrupt these interactions, but the effects of disruption on invasive plant performance and the underpinning mechanisms are poorly understood. Here, we used rainout shelters in an experimental field setting to test the hypothesis that drought reduces invasive plant performance by reducing microbial metabolic activity, resulting in decreased nitrogen flow to plants. We imposed growing season drought on populations of the exotic grass Microstegium vimineum, a widespread invasive plant in eastern deciduous forests, and quantified effects on aboveground and belowground biomass, and carbon (C) and nitrogen (N) cycling among plants, decomposers, and soil. Drought resulted in a 24% decrease in soil respiration, a 16% decrease in phenol oxidase enzyme activity, a 12% decrease in dissolved organic N concentration, and a decrease in the C:N ratio of particulate organic matter, suggesting reduced microbial metabolic activity and nutrient mining of soil organic matter. Drought also reduced aboveground Microstegium biomass 33% and increased Microstegium leaf C:N ratio, consistent with a decline in plant N uptake. We conclude that drought can reduce the performance of existing invasive species populations by suppressing plant-microbe interactions that increase nitrogen supply to plants, which may have consequences for the persistence of invasive plants under hydrologic change.

Microbial ecology of vertebrate decomposition in terrestrial ecosystems

Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.

Soil net N mineralization and hydraulic properties of carbonate-derived laterite under different vegetation types in Karst forests of China

Soil net nitrogen (N) mineralization (N_min) is a key process in the forest N cycle regulating the N availability of plant growth. However, it is unclear how N transformation responds to soil hydraulic properties changes. The soil inorganic N pools and N transformation in the early growing season in karst forestlands were investigated by using an intact soil core in situ incubation method. Three different typical vegetation types were selected. The results showed that the mean values of NH₄⁺-N, NO₃^--N, and inorganic N were 1.05-1.36, 1.55-3.85, and 1.05-2.34 times greater for ferns than for shrubs. NO₃^--N and NH₄⁺-N mainly occur at soil depths of 0-5 cm and 5-15 cm, respectively. The soil N_min was 2.21-232.03 times higher at 0-5 cm than at the 10-15 cm. Net N immobilization was found for the juvenile ferns and shrubs at 5-15 cm. The N_min of juvenile and mature ferns was 1.90-11.78 times and 1.17-16.20 times higher than shrubs, respectively, and shrubs had the highest K_s (69.91 mm h^-1) but the lowest water-holding capacity. Both ferns and shrubs were able to hold more water and available water was richest in mature fern soil, which provided an extra water source for fern growth. Principal component analysis (PCA) was used to test whether the measured variables affected N_min, and the results showed that soil organic matter (SOM), pH, and saturated volumetric water content (θ_s) were the main soil factors affecting N_min. In addition, the NH₄⁺-N, NO₃^--N, and inorganic N stocks were reduced by 3.98 %-59.04 %, 48.07 %-63.30 % and 8.18 %-57.37 % after rainwater input, respectively. Our findings suggest that soil inorganic N and N_min in the karst forest were regulated by soil hydraulic properties. Changes in the soil hydraulic properties might therefore influence the functioning of soil N transformation.

Architecture Optimization of a Non-Linear Autoregressive Neural Networks for Mackey-Glass Time Series Prediction Using Discrete Mycorrhiza Optimization Algorithm

Recurrent Neural Networks (RNN) are basically used for applications with time series and sequential data and are currently being used in embedded devices. However, one of their drawbacks is that RNNs have a high computational cost and require the use of a significant amount of memory space. Therefore, computer equipment with a large processing capacity and memory is required. In this article, we experiment with Nonlinear Autoregressive Neural Networks (NARNN), which are a type of RNN, and we use the Discrete Mycorrhizal Optimization Algorithm (DMOA) in the optimization of the NARNN architecture. We used the Mackey-Glass chaotic time series (MG) to test the proposed approach, and very good results were obtained. In addition, some comparisons were made with other methods that used the MG and other types of Neural Networks such as Backpropagation and ANFIS, also obtaining good results. The proposed algorithm can be applied to robots, microsystems, sensors, devices, MEMS, microfluidics, piezoelectricity, motors, biosensors, 3D printing, etc.

Quantifying the effect of the nitrogen biogeochemical processes on the distribution of ammonium in the riverbank filtration system

Ammonium (NH₄⁺) enrichment of riverbank filtration (RBF) systems is gaining popularity. However, most previous research has concentrated on NO₃^- removal efficiencies, while the mechanisms of NH₄⁺ enrichment remain unknown. A nitrogen biogeochemical process model was developed for the quantitative analysis of NH₄⁺ enrichment in the Kaladian well field in northwest Songyuan City, NE China. Data from laboratory experiments and in-situ monitoring were used to determine initial values and calibrate the thermodynamic/kinetic parameters representing nitrogen (N) biogeochemical reactions. (1) The NO₃^- from river was subjected to denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) within 10-14 m of the shore, whereas the NH₄⁺ in groundwater was caused by DNRA, organic nitrogen mineralization (MIN), and mixing with laterally recharged high NH₄⁺ groundwater. (2) DNF and DNRA were regulated by hydrodynamic processes, with the ranges of these processes being more significant in the wet season due to a higher hydraulic gradient. MIN occurred widely throughout the water flow path, with temperature primarily controlling the rates of the three reactions. (3) DNRA activity was relatively higher in the wet season when the water temperature was higher within 10-14 m of the shore. In the wet season, DNRA contributed 25%-30% to NO₃^- reduction, which was higher than in the dry season (5%-10%). DNRA contributed at least 40% and 15% to NH₄⁺ enrichment in the wet and dry seasons, respectively. (4). Organic N in media gradually released NH₄⁺ into groundwater via MIN and desorption across the entire flow path, with contributions to NH₄⁺ enrichment reaching 75% and 85%, respectively, in the wet and dry seasons.

Response strategies of fine root morphology of Cupressus funebris to the different soil environment

Understanding fine root morphology is crucial to uncover water and nutrient acquisition and transposition of fine roots. However, there is still a lack of knowledge regarding how the soil environment affects the fine root morphology of various root orders in the stable forest ecosystem. Therefore, this experiment assessed the response strategies of fine root morphology (first- to fifth -order fine roots) in four different soil environments. The results showed that fine root morphology was related to soil environment, and there were significant differences in specific root length (SRL), specific surface area (SRA), diameter (D), and root tissue density (RTD) of first- and second -order fine roots. Soil total nitrogen (TN), alkaline nitrogen (AN) and available phosphorus (AP) were positively correlated with SRL and SRA and negatively correlated with D and RTD. Soil moisture (SW) was positively correlated with the D and RTD of first- and second-order fine roots and negatively correlated with the SRL and SRA. Soil temperature (ST), organic carbon (OC), soil bulk density (SBD) and soil porosity (SP) were not significantly correlated with the D, SRL, SRA, and RTD of the first- and second -order fine roots. AN was positively correlated with SRL and SRA and negatively correlated with both D and RTD in the first- and second -order fine roots, and the correlation coefficient was very significant. Therefore, we finally concluded that soil AN was the most critical factor affecting root D, SRL, SRA and RTD of fine roots, and mainly affected the morphology of first- and second -order fine roots. In conclusion, our research provides support for understanding the relationship between fine root morphology and soil environment, and indicates that soil nutrient gradient forms good root morphology at intraspecific scale.

Potential Roles of Soil Microorganisms in Regulating the Effect of Soil Nutrient Heterogeneity on Plant Performance

The spatially heterogeneous distribution of soil nutrients is ubiquitous in terrestrial ecosystems and has been shown to promote the performance of plant communities, influence species coexistence, and alter ecosystem nutrient dynamics. Plants interact with diverse soil microbial communities that lead to an interdependent relationship (e.g., symbioses), driving plant community productivity, belowground biodiversity, and soil functioning. However, the potential role of the soil microbial communities in regulating the effect of soil nutrient heterogeneity on plant growth has been little studied. Here, we highlight the ecological importance of soil nutrient heterogeneity and microorganisms and discuss plant nutrient acquisition mechanisms in heterogeneous soil. We also examine the evolutionary advantages of nutrient acquisition via the soil microorganisms in a heterogeneous environment. Lastly, we highlight a three-way interaction among the plants, soil nutrient heterogeneity, and soil microorganisms and propose areas for future research priorities. By clarifying the role of soil microorganisms in shaping the effect of soil nutrient heterogeneity on plant performance, the present study enhances the current understanding of ecosystem nutrient dynamics in the context of patchily distributed soil nutrients.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

BACKGROUND

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS

Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to ¹³C-AMF hyphosphere DNA from a ¹³CO₂ plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% ¹³C), even though the soils' overall enrichment was low (1.8 atom% ¹³C). We assembled 212 ¹³C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived ¹³C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS

Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

Zinc application promotes nitrogen transformation in rice rhizosphere soil by modifying microbial communities and gene expression levels

Application of Zn fertilizers to agricultural field is a simple and effective way for farmers to manage Zn deficient stress in soils to avoid yield lose. Although a synergistic effect of Zn on N transformation in soil has been reported, the mechanism is not fully understood yet. In this study, we planted rice in soils with different combinations of Zn and N supply, and analyzed the plant growth and N uptake, the N transformation, microbial communities, enzyme activities and gene expression levels in rhizosphere soil to reveal the underlying mechanism. Results showed that Zn application promoted the rice growth and N uptake, increased the soil alkali-hydrolyzed N and NH₄⁺, but decreased NO₃^- and inhibited NH₃ volatilization from the rhizosphere soil under optimal N condition. Zn supply significantly increased the relative abundances of Sphingomonas, Gaiella, subgroup_6, and Gemmatimonas, but decreased nitrosifying bacteria Ellin6067; while increased saprophytic fungi Schizothecium and Mortierella, but decreased pathogenic fungi Gaeumannomyces, Acremonium, Curvularia, and Fusarium in the rhizosphere soil under optimal N condition. Meanwhile, Zn application elevated the activities of protease, cellulase and dehydrogenase, and up-regulated the expression levels of napA, nirS, cnorB, and qnorB genes involved in the denitrification process in rice rhizosphere soil under optimal N condition. These results indicated Zn application could facilitate the soil N transformation and improved its availability by modifying both bacterial and fungal communities, and altering the soil enzyme activities and functional gene expression levels, ultimately promoted the N uptake and biomass of rice plant. However, this synergistic effect of Zn on rice growth, N uptake and soil N transformation strongly depended on the external N conditions, as no significant changes were observed under high N condition. Our results indicated that Zn co-fertilized with appropriate application of N is a useful strategy to improve the N bioavailability in rice rhizosphere soil and enhance the N uptake in rice plant.

Greenhouse gas fluxes (CO2, N2O and CH4) of pea and maize during two cropping seasons: Drivers, budgets, and emission factors for nitrous oxide

Agriculture contributes considerably to the increase of global greenhouse gas (GHG) emissions. Hence, magnitude and drivers of temporal variations in carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) fluxes in croplands are urgently needed to develop sustainable, climate-smart agricultural practices. However, our knowledge of GHG fluxes from croplands is still very limited. The eddy covariance technique was used to quantify GHG budgets and N2O emission factors (EF) for pea and maize in Switzerland. The random forest technique was applied for gap-filling N2O and CH4 fluxes as well as to determine the relevance of environmental, vegetation vs. management drivers of the GHG fluxes during two cropping seasons. Environmental (i.e., net radiation, soil water content, soil temperature) and vegetation drivers (i.e., vegetation height) were more important drivers for GHG fluxes at field scale than time since management for the two crop species. Both crops acted as GHG sinks between sowing and harvest, clearly dominated by net CO2 fluxes, while CH4 emissions were negligible. However, considerable N2O emissions occurred in both crop fields early in the season when crops were still establishing. N2O fluxes in both crops were small later in the season when vegetation was tall, despite high soil water contents and temperatures. Results clearly show a strong and highly dynamic microbial-plant competition for N driving N2O fluxes at the field scale. The total loss was 1.4 kg N2O-N ha-1 over 55 days for pea and 4.8 kg N2O-N ha-1 over 127 days for maize. EFs of N2O were 1.5 % (pea) and 4.4 % (maize) during the cropping seasons, clearly exceeding the IPCC Tier 1 EF for N2O. Thus, sustainable, climate-smart agriculture needs to consider crop phenology and better adapt N supply to crop N demand for growth, particularly during the early cropping season when competition for N between establishing crops and soil microorganisms modulates N2O losses.

Rapid Permafrost Thaw Removes Nitrogen Limitation and Rises the Potential for N2O Emissions

Ice–rich Pleistocene permafrost deposits (Yedoma) store large amounts of nitrogen (N) and are susceptible to rapid thaw. In this study, we assess whether eroding Yedoma deposits are potential sources of N and gaseous carbon (C) losses. Therefore, we determined aerobic net ammonification and nitrification, as well as anaerobic production of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) in laboratory incubations. Samples were collected from non-vegetated and revegetated slump floor (SF) and thaw mound (TM) soils of a retrogressive thaw slump in the Lena River Delta of Eastern Siberia. We found high nitrate concentrations (up to 110 µg N (g DW)−1) within the growing season, a faster transformation of organic N to nitrate, and high N2O production (up to 217 ng N2O-N (g DW)−1 day−1) in revegetated thaw mounds. The slump floor was low in nitrate and did not produce N2O under anaerobic conditions, but produced the most CO2 (up to 7 µg CO2-C (g DW)−1 day−1) and CH4 (up to 65 ng CH4-C (g DW)−1 day−1). Nitrate additions showed that denitrification was substrate limited in the slump floor. Nitrate limitation was rather caused by field conditions (moisture, pH) than by microbial functional limitation since nitrification rates were positive under laboratory conditions. Our results emphasize the relevance of considering landscape processes, geomorphology, and soil origin in order to identify hotspots of high N availability, as well as C and N losses. High N availability is likely to have an impact on carbon cycling, but to what extent needs further investigation.

Functional microbial ecology in arctic soils: the need for a year-round perspective

The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.

Isotopic and hydrogeochemical tracking of dissolved nutrient dynamics in the Brahmaputra River System: A source delineation perspective

The Brahmaputra river system (BRS) produces the largest discharge in India, supplying water to more than 62 million inhabitants. The present study aims to quantify the environmental elements that affect the spatio-temporal variation of nutrients in the Brahmaputra river system (BRS). The association of physico-chemical characteristics of floodplain sediments with the distribution pattern of P during wet and dry periods in different depths were also studied. The seasonal variation suggest that the average dissolved inorganic nitrogen and dissolve inorganic phosphorus are found higher in monsoon while the average dissolve silica were higher in post-monsoon. The spatial variation of dissolve inorganic phosphate and nitrate concentration suggests both the nutrient are higher in upstream sites. The DiS concentrations tended to be higher in downstream. In 70% of the sampled tributaries, the average molar ratio for dissolved inorganic nitrogen/dissolved inorganic phosphorous (DIN/DIP) was greater than 16:1, which indicates phosphate limited biological productivity. In contrast, an average molar ratio of dissolved inorganic silica/DIN (DSi/DIN) of 3.8 ± 3.0 favoured diatom growth in those tributaries where DSi/DIN molar ratio was lower than 1, indicating eutrophication. The BRS transported 24.7, 5.93, and 312 × 10⁴ tons/year^-1 of DIN, PO₄-P and SiO₂-Si, respectively. The depth-wise variation of P-fraction during monsoon suggests that the authigenic phosphorus was most abundant followed by Fe-bound, exchangeable, detrital and organic. In the post-monsoon, Fe-bound P was found at a higher concentration followed by authigenic phosphorus. High nutrient concentrations with more δ¹⁸O depleted water implied precipitation being the major source of nutrients in the BRS.

Soil mineral nitrogen regulation by a novel porous material in structurally degraded soils

BACKGROUND

The availability of soil nitrogen (N) decreases as the structure of agricultural soils degrades. Traditional methods focus on organic amendments that indirectly affect the porosity and N content of soil. Due to the low efficiency of such amendments, new materials, particularly highly porous materials, are needed to improve the quality of soil, which has opened new directions.

RESULTS

The addition of 2 to 7 mm of porous clay ceramic (PLC) significantly increased the fresh weight of Brassica chinensis. The soil aeration porosity (>50 μm) increased by 0.69% on average in response to 1% PLC application. Soil NO₃ ^- -N, NH₄ ⁺ -N and mineral N increased by 3.3, 1.3 and 4.6 mg kg^-1 on average, respectively, following a 1% PLC application rate. The initial N content of the high PLC treatments was the lowest in the incubation experiment. The parameters of soil N mineralization, i.e. potentially mineralizable N (N₀ ), the first-order rate constant (k) and the mineralization composite index (N₀  × k), increased obviously as the amount of PLC increased. Porosities larger than 1000 μm were significantly more positively correlated with the parameters of soil N mineralization than those <500 μm. The Pearson correlation coefficients suggested that high porosity, mineral N and N₀ values had significant positive relationships with the fresh weights in double seasons.

CONCLUSION

The application of PLC increased soil aeration and enhanced the availability of soil N, which yielded large vegetable harvests in clayey soils in the short term. © 2022 Society of Chemical Industry.